Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone

Metabolic Preference for Denitrification over O₂ Respiration.

Our results reveal a positive correlation of the individual rates of denitrification and O₂ respiration to the cell volume as described by the power law equations Eqs. 1 and 2 (Figs. 1A and 2A). These equations are a valuable tool to further constrain foraminiferal denitrification and O₂ respiration rates in biogeochemical models for marine NO₃⁻ and C cycling. Data for species-specific rates of benthic foraminifera are limited in the literature. Additionally, the scaling of such functions can be used to determine if foraminifera have a metabolic preference for denitrification or O₂ respiration. The exponent in the power law relationship between foraminiferal O₂ respiration and cell volume (Eq. 2) is sublinear (α < 1). Such sublinear metabolic scaling can be found for a wide range of organisms (40, 41). A recent study argued that the sublinear scaling (α < 1) does not extend to protists (α, ∼1) (39). However, foraminifera are relatively large protists, where the bigger species overlap in size with many metazoans. The metabolic rates observed in large protists and small metazoans are similar as well. Consequently, it has been hypothesized that the decrease in metabolic scaling in large protists is related to the increased demand of electron acceptors to the respiratory complexes. In large protists, the cell volume and number of mitochondria are increased; however, their cell surface area is a limiting factor for the uptake of resources from the environment (39). The Peruvian OMZ is one of the most O₂-depleted regions in the world’s oceans (42). Indeed, the O₂ respiration rates of foraminifera from the Peruvian OMZ scale with the cell volume with a much lower exponent (α = 0.41; Fig. 2A) in comparison with the dataset from an earlier study, which mostly contains species from more oxygenated environments (from ref. 36 excluding our data from Peru: α = 0.80). Consequently, we conclude that the Peruvian species metabolize O₂ less efficiently compared with species from other regions. We further show that the exponent for individual denitrification (α = 0.68, Fig. 1A) is higher than the exponent calculated for O₂ respiration in the Peruvian species (α = 0.41; Fig. 2A). This indicates that denitrification is more efficient than O₂ respiration in species from the Peruvian OMZ.

The foraminiferal volume-specific O₂ respiration rate significantly decreases with cell volume (Fig. 2B). This finding is in agreement with earlier reports in the literature (33). We suggest that this negative correlation is related to the decrease of the surface/volume ratio with increasing cell volume, which is a limiting factor for O₂ uptake. Indeed, the volume-specific O₂ respiration rates were positively correlated with the individual surface/volume ratio (Fig. 4). Notably, the volume-specific O₂ respiration rate of the Peruvian species decreased with cell volume with a steeper slope compared with the general trend found for foraminifera, including species from oxygenated habitats (Fig. 2B). This indicates that the Peruvian species are unable to sustain an increased O₂ supply with an increase in cell size. However, we note that the O₂ respiration rates we measured here are potential rates because most of the presented Peruvian species reside within a permanently anoxic habitat. Our results further revealed that the volume-specific O₂ respiration rates of the Peruvian species scales more strongly with their cell volume and their surface/volume ratio in comparison with their volume-specific denitrification rate (Figs. 1B, 2B, and 4). This might be explained by the supply pathway of the two electron acceptors to the respiratory complex. Since O₂ cannot be stored in the cell, its supply depends on the environmental [O₂]. In contrast, NO₃⁻ is readily available for denitrification through the intracellular NO₃⁻ storage. Consequently, the rate of denitrification is not expected to decrease in bigger cells due to a decrease in surface to volume ratio. We further hypothesize that the foraminifers even overcome the limitation of electron acceptor supply imposed by the outer cell surface area, by performing denitrification. The enigmatic observation that the cell volume of some foraminiferal species from the Santa Barbara Basin is negatively correlated with [O₂] (43) can be explained by this availability of an alternative electron acceptor storage. Indeed, several foraminifera in that habitat have been shown to denitrify (18).

Foraminiferal Ecology and the Availability of Electron Acceptors.

Our results indicate that the preference of denitrification over O₂ respiration strongly relies on the microhabitat of the foraminiferal species. The microhabitat is, among other parameters, characterized by different ratios of the electron acceptors NO₃⁻ and O₂ in the environment. Based on our findings, we propose a conceptual biogeochemical model describing foraminiferal denitrification in OMZs according to the environmental [NO₃⁻]/[O₂] ratio (Fig. 5; details in SI Appendix, Note 1). Foraminifera residing in the upper boundary of the Peruvian OMZ (Fig. 5A) showed a relatively low ratio of denitrification/O₂ respiration (Fig. 3B). The upper OMZ boundary is a highly fluctuating environment where the oxycline can vary between 0–125 m and strong O₂ intrusions from above are common at these water depths (44, 45). The bottom water [NO₃⁻] is relatively low (SI Appendix, Figs. S4 and S5) and can, during sulfidic events, be completely consumed (25) (SI Appendix, Fig. S6). Furthermore, mats of sulfur bacteria capable of performing DNRA are often clustered around the upper OMZ boundary (25, 46); hence, the competition for NO₃⁻ uptake in this region may be intense. The most common foraminiferal species living in these depths is the small B. costata (cell volume between 2 × 10⁵ and 10 × 10⁵ µm³; n = 67). This species is characteristic for sulfidic sediments containing high amounts of labile organic matter, but it can also thrive in well-oxygenated sediments (45). From previous observations of B. costata (45), we can assert that species at the upper OMZ boundary are well adapted to fluctuations of the oxycline, periodic sulfidic conditions, and limited NO₃⁻ availability. In summary, foraminifera thriving in this environment are small, have a low ratio of denitrification/O₂ respiration, and, thus, generally have a low denitrification capacity, even if they occur in high abundances (Fig. 5A).

• Download figure
• Open in new tab
• Download powerpoint

Fig. 5.

Conceptual model for benthic foraminiferal denitrification at the Peruvian OMZ. A detailed description of the model is presented in SI Appendix, Note 1. (A) Upper OMZ boundary within the lower productive mixed layer: high C_org fluxes and O₂ consumption, low [NO₃⁻], high foraminiferal abundances, small foraminifera → Low [NO₃⁻]/[O₂] ratios and low total benthic foraminiferal denitrification. (B) Anoxic OMZ core: C_org fluxes decrease with water depth due to remineralization, while [NO₃⁻] increases, which results in larger foraminifera. Depletion of O₂ facilitates C_org preservation in the sediments, causing increased foraminiferal abundances. All this causes high [NO₃⁻]/[O₂] ratios and high total benthic foraminiferal denitrification, both increasing with water depth. (C) Lower OMZ boundary: C_org fluxes are decreasing because most C_org is already remineralized in the water column above. While [O₂] gradually increases with water depth, [NO₃⁻] reaches a plateau. Foraminiferal abundances decrease due to decreased C_org within the sediments. This results in a sharp decrease of [NO₃⁻]/[O₂] ratios and total benthic foraminiferal denitrification with water depth. [NO₃⁻] and [O₂] have been schematized after the data shown in the SI Appendix, Fig. S4.

In contrast, foraminifera thriving at the lower OMZ boundary (Fig. 5C) have a relatively high denitrification/O₂ respiration ratio, indicating that they metabolize NO₃⁻ more efficiently than O₂. Indeed, the [O₂] below the OMZ are variable, but only weakly, below 500 m water depth (47). The bottom water in these depths is considered to be anoxic most of the time (see also Fig. 3A and SI Appendix, Figs. S5A and S6B). Additionally, the [NO₃⁻] is relatively high at these depths due to the increase of [NO₃⁻] with water depth (SI Appendix, Fig. S5C). Competition for NO₃⁻ is restricted to the present foraminifers and to denitrifying bacteria. Some of the foraminiferal species present at these depths, e.g., Cancris carmenensis or Valvulineria inflata, can reach relatively large cell volumes (between 100 × 10⁵ and 1,000 × 10⁵ µm³, n = 24). Notably, the intracellular NO₃⁻ uptake rate of foraminifera can be 10-fold higher than the denitrification rate (10). This observation further supports our notion according to which there is no limitation of electron acceptor uptake through the surface/volume ratio due to the availability of an intracellular NO₃⁻ storage. In summary, foraminifera can grow larger with increasing NO₃⁻ availability (thus water depth) and have an increasing denitrification capacity (Fig. 5 B and C).

The species-specific ratio of denitrification/O₂ respiration for the most abundant species at the Peruvian OMZ is directly coupled to the availability of NO₃⁻ and O₂ within their habitat (Fig. 3B). Our results indicate that the availability of different electron acceptors influences the community structure, and thus the ecology of benthic foraminifera. Even within individual species, the cell volume can be a plastic phenotypic trait that can depend on the electron acceptor concentration in the environment, as shown for B. seminuda (SI Appendix, Fig. S3). Benthic foraminifera are known to widely disperse as small juveniles or propagules and to form propagule banks in sediments (48). These banks contain abundant and diverse foraminiferal propagules that grow to maturity when exposed to the appropriate environmental conditions (48, 49). We hypothesize that the availability of different electron acceptors constitutes an additional selecting factor for the composition of species that develop from a propagule bank, in addition to other factors such as water depth, salinity, pH, and organic matter (C_org) supply. Indeed, the influence of O₂ and C_org on the distribution of foraminifera in benthic microhabitats has been described by the conceptual trophic oxygen model (50). A later study pointed out that the influence of alternative electron acceptors (NO₃⁻ in particular) (51) should be considered as well. Thus, species having high species-specific denitrification rates, like C. carmenensis and V. inflata, could develop when [NO₃⁻] is high and competition for NO₃⁻ uptake is low. Other species can grow to larger cell size due to increased [NO₃⁻] (SI Appendix, Fig. S3B). Such a community composition might lead to increased denitrification in the habitat. Furthermore, in habitats where NO₃⁻ is scarce and competition for NO₃⁻ uptake high (e.g., due to the presence of sulfur bacteria), species with a low species-specific denitrification rates (i.e., smaller species) would be favored. Consequently, the total foraminiferal denitrification is expected to decrease as NO₃⁻ availability will become a limiting factor for the total benthic denitrification. Our data, in combination with data of an earlier study (23) suggest that the ratio of foraminiferal denitrification over bacterial denitrification is around 20–50% within the Peruvian OMZ core but only 5% below the lower OMZ boundary (SI Appendix, Note 2 and Table S8).